{"database": "metadata", "table": "run_metadata", "rows": [[33294, "SRR29920543", "SRX25414719", "SRS22075127", "SRP521426", "PRJNA1138768", "Gonadotropin releasing hormone 3 and gonadotropes relationships in female zebrafish pituitary revealed by single cell transcriptomics", "GSE272806", "Transcriptome Analysis", "Gonadotropin releasing hormone GnRH governs reproduction in vertebrates by regulating pituitary gonadotropins. Zebrafish  however  is an exception as gnrh3\u2013/\u2013 fish  which lack the hypophysiotropic GnRH3  are fertile  suggesting that zebrafish utilizes a Gnrh independent mechanism to regulate reproduction. To elucidate the role of Gnrh3 and the Gnrh independent mechanisms that regulate the pituitary gonadotropes  we profiled the gene expression in individual pituitary cells of wild type and gnrh\u2013/\u2013 adult female zebrafish and identified transcriptionally defined cell types. The classical Lh and Fsh gonadotropes expressed both gonadotropin beta subunits with a ratio of 13:1 lhb:fshb and 40:1 fshb:lhb  respectively. We discovered that Lh gonadotropes predominantly express genes encoding receptors for Gnrh gnrhr2  thyroid hormone  estrogen  dopamine  and steroidogenic factor 1 SF1. No Gnrh receptor expression was enriched in Fsh gonadotropes  instead  the expression of cholecystokinin receptor cckrb and galanin receptor gal1rb were enriched in these cells. The hereditary loss of Gnrh3 gene resulted in downregulation of fshb in Lh gonadotropes. Likewise  targeted chemogenetic ablation of Gnrh3 neurons led to a decrease in the number of fshb+/lhb+ cells. Our studies suggest that Gnrh3 directly acts on Lh gonadotropes through Gnrhr2  but the outcome of this interaction is still unknown. Gnrh3 also regulates fshb expression  probably via a non Gnrh receptor route. Altogether  while Lh secretion and synthesis are likely regulated by multiple factors in a Gnrh independent manner  Gnrh3 seems to play a role in the cellular organization of the pituitary in zebrafish. Overall design: Pituitaries of WT and Gnrh3 knockout female zebrafish were dissociated and analyzed using single cell RNA sequencing", null, "pubmed:39499852", null, "gnrh3 knockout  scRNAseq", "GSM8412848", null, "source name:Pituitary|tissue:Pituitary|age:Adult 3 mpf|genotype:gnrh3 / |Sex:female|geo loc name:missing|collection date:missing", "gnrh3 knockout  scRNAseq", "Barcode processing and gene counting were made using the 10\u00d7Genomics Cell Ranger v6.0.2 software. Quality control  normalization  data integration  and clustering were performed using Seurat v4 R package. Assembly: GRCz11/danRer11 Supplementary files format and content: Tab separated values files  matrix file  and comma separated values file", "Pituitary", null, "Five pituitaries were dissected from each gnrh3\u2013/\u2013 and WT females at 8 00 h which was 1 hour before lights on. The dissected pituitaries were pooled by genotype in a 1.5 mL Eppendorf tube filled with sterile phosphate buffered saline PBS and left on ice until processing. Pituitary dissociation was performed by following previously described protocols in Hollander Cohen et al 2021 and Fabian et al 2020 with some modifications. Briefly  the samples were centrifuged at 2 000 \u00d7 rpm for 5 minutes at 4\u00b0C  then PBS was removed followed by a treatment of dissociation solution 0.25% Trypsin; 1 mM EDTA; 0.2% collagenase in PBS; filtered with a 0.22 \u00b5m membrane filter at 28.5\u00b0C for 40 minutes  with gently pipetting every 10 minutes using a wide bore tip. post incubation  the treatment was stopped by adding 200 \u00b5L 6\u00d7Stop solution [6 mM CaCl2; 30% fetal bovine serum FBS in PBS] and gently mixed it by pipetting  followed by centrifuging at 2 000 \u00d7 rpm for 5 minutes at 4\u00b0C. The supernatant was gently discarded  then 1 mL Accumax working solution 30% Accumax in PBS was added  and the cells were gently resuspended. post incubation at room temperature for 5 minutes  the dissociated cells were filtered through 40 \u00b5m pore cell strainer. post centrifuging at 2 000 \u00d7 rpm for 5 minutes at 4\u00b0C  the supernatant was removed  and the cell pellets were gently resuspended with 50 \u00b5L 0.1% BSA in PBS and kept on ice until processing. cDNA libraries were prepared using 10\u00d7Genomics Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 on the 10\u00d7Genomics Chromium Controller according to the manufacturer\u2019s manual for a target of 4 000 cells per sample.", null, "tissue:Pituitary|age:Adult 3 mpf|genotype:gnrh3 / |Sex:female", "GSM8412848", "GSM8412848: gnrh3 knockout  scRNAseq; Danio rerio; RNA Seq", "GSM8412848 r1", "GSM8412848", "1", "Five pituitaries were dissected from each gnrh3\u2013/\u2013 and WT females at 8 00 h which was 1 hour before lights on. The dissected pituitaries were pooled by genotype in a 1.5 mL Eppendorf tube filled with sterile phosphate buffered saline PBS and left on ice until processing. Pituitary dissociation was performed by following previously described protocols in Hollander Cohen et al 2021 and Fabian et al 2020 with some modifications. Briefly  the samples were centrifuged at 2 000 \u00d7 rpm for 5 minutes at 4\u00b0C  then PBS was removed followed by a treatment of dissociation solution 0.25% Trypsin; 1 mM EDTA; 0.2% collagenase in PBS; filtered with a 0.22 \u00b5m membrane filter at 28.5\u00b0C for 40 minutes  with gently pipetting every 10 minutes using a wide bore tip. post incubation  the treatment was stopped by adding 200 \u00b5L 6\u00d7Stop solution [6 mM CaCl2; 30% fetal bovine serum FBS in PBS] and gently mixed it by pipetting  followed by centrifuging at 2 000 \u00d7 rpm for 5 minutes at 4\u00b0C. The supernatant was gently discarded  then 1 mL Accumax working solution 30% Accumax in PBS was added  and the cells were gently resuspended. post incubation at room temperature for 5 minutes  the dissociated cells were filtered through 40 \u00b5m pore cell strainer. post centrifuging at 2 000 \u00d7 rpm for 5 minutes at 4\u00b0C  the supernatant was removed  and the cell pellets were gently resuspended with 50 \u00b5L 0.1% BSA in PBS and kept on ice until processing. cDNA libraries were prepared using 10\u00d7Genomics Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 on the 10\u00d7Genomics Chromium Controller according to the manufacturer's manual for a target of 4 000 cells per sample.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP521426", null, "loader:fastq load.py", "KO_20210616_A00904_IL100185604_S1_L001_I1_001.fastq.gz KO_20210616_A00904_IL100185604_S1_L001_I2_001.fastq.gz KO_20210616_A00904_IL100185604_S1_L001_R1_001.fastq.gz KO_20210616_A00904_IL100185604_S1_L001_R2_001.fastq.gz", "fastq fastq fastq fastq", 27063230346.0, 121906443.0, "GSM8412848 r1", "0:10 1:10 2:101 3:101", "A:6434793761;C:4051189285;G:4401327014;T:9737249538;N:541888", 10, 10, 101, 101, 6434793761, 4051189285, 4401327014, 9737249538, 541888, "SRX25414719", "SRS22075127", "SRA1930291", "Stanford University", "Stanford University", 2, 0.10559, 0.92046, 0.02334, 0.15386, 0.97879, 0.81732, 0.68611, 0.62975, 101, 101, "T", "B", "mate1 technical by mapping diff", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United States", "2024-07-22", "Adult", "Adult", "Pituitary Gland", "Endocrine System"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["33294"], "units": {}, "query_ms": 9.865610001725145}